git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15129 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -42,19 +42,20 @@ the reaction rate equation is defined to be of the form
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.. image:: Eqs/fix_rx_reactionRate.jpg
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:align: center
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In the current implementation, the exponents are defined to be equal to the
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stoichiometric coefficients. A given reaction set consisting of *n* reaction
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equations will contain a total of *m* species. A set of *m* ordinary
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differential equations (ODEs) that describe the change in concentration of a
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given species as a function of time are then constructed based on the *n*
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reaction rate equations.
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In the current implementation, the exponents are defined to be equal
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to the stoichiometric coefficients. A given reaction set consisting
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of *n* reaction equations will contain a total of *m* species. A set
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of *m* ordinary differential equations (ODEs) that describe the change
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in concentration of a given species as a function of time are then
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constructed based on the *n* reaction rate equations.
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The ODE systems are solved over the full DPD timestep *dt* using a 4th order
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Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified by the
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*lammps_rk4* keyword. The number of ODE steps per DPD timestep for the rk4 method
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is optionally specified immediately after the rk4 keyword. The ODE step-size is set as
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*dt/num_steps*\ . Smaller step-sizes tend to yield more accurate results but there
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is not control on the error.
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The ODE systems are solved over the full DPD timestep *dt* using a 4th
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order Runge-Kutta *rk4* method with a fixed step-size *h*\ , specified
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by the *lammps_rk4* keyword. The number of ODE steps per DPD timestep
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for the rk4 method is optionally specified immediately after the rk4
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keyword. The ODE step-size is set as *dt/num_steps*\ . Smaller
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step-sizes tend to yield more accurate results but there is not
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control on the error.
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----------
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@ -64,28 +65,30 @@ The filename specifies a file that contains the entire set of reaction
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kinetic equations and corresponding Arrhenius parameters. The format of
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this file is described below.
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There is no restriction on the total number or reaction equations that are
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specified. The species names are arbitrary string names that are associated
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with the species concentrations.
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Each species in a given reaction must be preceded by it's stoichiometric
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coefficient. The only delimiters that are recognized between the species are
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either a *+* or *=* character. The *=* character corresponds to an
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irreversible reaction. After specifying the reaction, the reaction rate
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constant is determined through the temperature dependent Arrhenius equation:
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There is no restriction on the total number or reaction equations that
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are specified. The species names are arbitrary string names that are
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associated with the species concentrations. Each species in a given
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reaction must be preceded by it's stoichiometric coefficient. The
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only delimiters that are recognized between the species are either a
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*+* or *=* character. The *=* character corresponds to an
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irreversible reaction. After specifying the reaction, the reaction
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rate constant is determined through the temperature dependent
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Arrhenius equation:
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.. image:: Eqs/fix_rx.jpg
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:align: center
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where *A* is the Arrhenius factor in time units or concentration/time units,
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*n* is the unitless exponent of the temperature dependence, and *E_a* is the
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activation energy in energy units. The temperature dependence can be removed
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by specifying the exponent as zero.
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where *A* is the Arrhenius factor in time units or concentration/time
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units, *n* is the unitless exponent of the temperature dependence, and
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*E_a* is the activation energy in energy units. The temperature
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dependence can be removed by specifying the exponent as zero.
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The internal temperature of the coarse-grained particles can be used in constructing the
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reaction rate constants at every DPD timestep by specifying the keyword *none*\ .
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Alternatively, the keyword *lucy* can be specified to compute a local-average particle
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internal temperature for use in the reaction rate constant expressions.
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The local-average particle internal temperature is defined as:
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The internal temperature of the coarse-grained particles can be used
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in constructing the reaction rate constants at every DPD timestep by
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specifying the keyword *none*\ . Alternatively, the keyword *lucy* can
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be specified to compute a local-average particle internal temperature
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for use in the reaction rate constant expressions. The local-average
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particle internal temperature is defined as:
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.. image:: Eqs/fix_rx_localTemp.jpg
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:align: center
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@ -101,7 +104,8 @@ The self-particle interaction is included in the above equation.
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----------
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The format of a tabulated file is as follows (without the parenthesized comments):
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The format of a tabulated file is as follows (without the
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parenthesized comments):
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.. parsed-literal::
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@ -118,21 +122,23 @@ A section begins with a non-blank line whose 1st character is not a
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"#"; blank lines or lines starting with "#" can be used as comments
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between sections.
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Following a blank line, the next N lines list the N reaction equations.
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Each species within the reaction equation is specified through its
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stoichiometric coefficient and a species tag. Reactant species are specified
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on the left-hand side of the equation and product species are specified on the
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right-hand side of the equation. After specifying the reactant and product
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species, the final three arguments of each line represent the Arrhenius
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parameter *A*\ , the temperature exponent *n*\ , and the activation energy *Ea*\ .
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Following a blank line, the next N lines list the N reaction
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equations. Each species within the reaction equation is specified
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through its stoichiometric coefficient and a species tag. Reactant
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species are specified on the left-hand side of the equation and
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product species are specified on the right-hand side of the equation.
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After specifying the reactant and product species, the final three
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arguments of each line represent the Arrhenius parameter *A*\ , the
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temperature exponent *n*\ , and the activation energy *Ea*\ .
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Note that the species tags that are defined in the reaction equations are
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used by the :doc:`fix eos/table/rx <fix_eos_table_rx>` command to define the
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thermodynamic properties of each species. Furthermore, the number of species
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molecules (i.e., concentration) can be specified either with the :doc:`set <set>`
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command using the "d_" prefix or by reading directly the concentrations from a
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data file. For the latter case, the :doc:`read_data <read_data>` command with the
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fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a <SPECIES">`_ suffix, e.g.
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Note that the species tags that are defined in the reaction equations
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are used by the :doc:`fix eos/table/rx <fix_eos_table_rx>` command to
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define the thermodynamic properties of each species. Furthermore, the
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number of species molecules (i.e., concentration) can be specified
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either with the :doc:`set <set>` command using the "d_" prefix or by
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reading directly the concentrations from a data file. For the latter
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case, the :doc:`read_data <read_data>` command with the fix keyword
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should be specified, where the fix-ID will be the "fix rx`ID with a <SPECIES">`_ suffix, e.g.
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fix foo all rx reaction.file ...
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read_data data.dpd fix foo_SPECIES NULL Species
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@ -145,11 +151,14 @@ Restrictions
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""""""""""""
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The fix *rx* is only available if LAMMPS is built with the USER-DPD package.
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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The fix *rx* must be used with the :doc:`atom_style dpd <atom_style>` command.
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This command also requires use of the :doc:`atom_style dpd <atom_style>`
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command.
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The fix *rx* can only be used with a constant energy or constant enthalpy DPD simulation.
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This command can only be used with a constant energy or constant
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enthalpy DPD simulation.
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Related commands
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""""""""""""""""
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@ -161,10 +170,6 @@ Related commands
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**Default:** none
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----------
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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